SAR247799-bound S1PR1-Gi protein complex
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8yic
Q-score: 0.448
Xu Z, Yu JJ, Wang KX, Yan W, Shao ZH
To Be Published
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Sar-247799-bound s1pr1 (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Gi heterotrimer (Complex from Homo sapiens)
- Endolysin,sphingosine 1-phosphate receptor 1 (58 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (41 kDa, Protein from Homo sapiens)
- Sar247799 (425 Da, Ligand)
- Sar247799-bound s1pr1 in complex with gi heterotrimer (Complex)
Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
Resolution: 2.0 Å
EM Method: Single-particle
Fitted PDBs: 9c3h
Q-score: 0.684
Zhu X, Cruz VE, Zhang H, Erzberger JP, Mendell JT
Science (2024) 386 pp. eadq8587-eadq8587 [ Pubmed: 39571015 DOI: doi:10.1126/science.adq8587 ]
- Small ribosomal subunit protein es27 (9 kDa, Protein from Homo sapiens)
- Nascent chain (3 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es28 (7 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us14 (6 kDa, Protein from Homo sapiens)
- Trna-arg,ccg-1 (24 kDa, RNA from Homo sapiens)
- Large ribosomal subunit protein ul23 (17 kDa, Protein from Homo sapiens)
- 5s rrna (38 kDa, RNA from Homo sapiens)
- Small ribosomal subunit protein es10 (18 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el39 (6 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul15 (16 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul24 (17 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el22 (14 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el38 (8 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el15 (24 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us7 (22 kDa, Protein from Homo sapiens)
- Fau ubiquitin-like and ribosomal protein s30 (14 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el33 (12 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es6 (28 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul5 (20 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el43 (10 kDa, Protein from Homo sapiens)
- 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol (282 Da, Ligand)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul13 (23 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el19 (23 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Large ribosomal subunit protein el32 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es17 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el29 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es32 (3 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es8 (24 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us11 (16 kDa, Protein from Homo sapiens)
- Ccr4-not transcription complex subunit 3 (64 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el42 (12 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us19 (17 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Large ribosomal subunit protein el28 (15 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el24 (17 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us4 (22 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us9 (16 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us13 (17 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el21 (18 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el37 (11 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es21 (9 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el14 (23 kDa, Protein from Homo sapiens)
- Isoform 3 of small ribosomal subunit protein es24 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el13 (24 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es4, x isoform (29 kDa, Protein from Homo sapiens)
- Mrna (2 kDa, RNA from Homo sapiens)
- Large ribosomal subunit protein el31 (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us12 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul2 (28 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul30 (29 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el6 (32 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es1 (30 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us10 (13 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul3 (46 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us2 (32 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us5 (31 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul22 (21 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el8 (30 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul29 (14 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us17 (18 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es19 (16 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul18 (34 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es25 (13 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- 28s rrna (1 MDa, RNA from Homo sapiens)
- Large ribosomal subunit protein ul14 (14 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul4 (47 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el20 (20 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el30 (12 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el40 (11 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es12 (14 kDa, Protein from Homo sapiens)
- 80s ribosome in complex with cnot3 and p-site trna arg ccg-1 (4 MDa, Complex from Homo sapiens)
- Large ribosomal subunit protein el36 (12 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es26 (13 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el18 (21 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein ul16 (24 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein es7 (22 kDa, Protein from Homo sapiens)
- 5.8s rrna (50 kDa, RNA from Homo sapiens)
- Large ribosomal subunit protein el27 (15 kDa, Protein from Homo sapiens)
- Large ribosomal subunit protein el34 (13 kDa, Protein from Homo sapiens)
- Small ribosomal subunit protein us15 (17 kDa, Protein from Homo sapiens)
- 18s rrna (603 kDa, RNA from Homo sapiens)
- Large ribosomal subunit protein ul6 (21 kDa, Protein from Homo sapiens)
heterodimer of mGlu2 and mGlu4 bound with mGlu2 agonist LY379268
Resolution: 5.95 Å
EM Method: Single-particle
Fitted PDBs: 8wgc
Q-score: 0.215
Huang W, Jin N, Guo J, Shen C, Xu C, Xi K, Bonhomme L, Quast RB, Shen DD, Qin J, Liu YR, Song Y, Gao Y, Margeat E, Rondard P, Pin JP, Zhang Y, Liu J
Nat Commun (2024) 15 pp. 10345-10345 [ DOI: doi:10.1038/s41467-024-54744-7 Pubmed: 39609406 ]
- (1r,4r,5s,6r)-4-azanyl-2-oxabicyclo[3.1.0]hexane-4,6-dicarboxylic acid (187 Da, Ligand)
- Metabotropic glutamate receptor 4 (98 kDa, Protein from Homo sapiens)
- Metabotropic glutamate receptor 2 (93 kDa, Protein from Homo sapiens)
- Heterodimer of mglu2 and mglu4 bound with mglu2 agonist ly379268 (Complex from Homo sapiens)
ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9dby
Q-score: 0.39
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Ncprc1rybp bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9dde
Q-score: 0.456
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Histone h3.2 (Complex from Xenopus laevis)
- Ncprc1-rybp (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a (Complex from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h4 (Complex from Xenopus laevis)
- Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histones (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ring2, ubiquitin-conjugating enzyme e2 d3 (Complex from Homo sapiens)
- Histone h1.4 (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (Complex from synthetic construct)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 9dg3
Q-score: 0.382
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ring1 and yy1-binding protein (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ncprc1rybp delta-linker mutant bound to singly modified h2ak119ub nucleosome (Complex from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
ncPRC1RYBP bound to unmodified nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 9dgg
Q-score: 0.47
Lopez VG, Valencia-Sanchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature (2024) 636 pp. 755-761 [ Pubmed: 39537923 DOI: doi:10.1038/s41586-024-08183-5 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb complex protein bmi-1 (37 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Ncprc1rybp bound to unmodified nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- E3 ubiquitin-protein ligase ring2 (37 kDa, Protein from Homo sapiens)
- Dna (187-mer) (57 kDa, DNA from synthetic construct)
Cryo-EM Structure of MILI-piRNA-target (8-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij0
Q-score: 0.417
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Rna (5'-r(p*gp*ap*up*gp*gp*up*ap*a)-3') (2 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Mili-pirna-target (8-nt) (Complex from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (22-nt, bilobed)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij1
Q-score: 0.325
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Mili-pirna-target (22-nt, bilobed) (Complex from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*gp*up*up*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*a)-3') (6 kDa, RNA from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (22-nt, comma)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 9ij2
Q-score: 0.188
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ DOI: doi:10.1038/s41586-024-08438-1 Pubmed: 39814893 ]
- Mili-pirna-target (22-nt, comma) (Complex from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*gp*up*up*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*a)-3') (6 kDa, RNA from Homo sapiens)
- Rna (5'-r(p*up*up*ap*cp*cp*ap*up*cp*ap*ap*cp*ap*up*gp*gp*ap*ap*ap*cp*up*up*g)-3') (6 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)